HEADER HYDROLASE 15-FEB-14 4OZE TITLE A.AOLICUS LPXC IN COMPLEX WITH NATIVE PRODUCT COMPND MOL_ID: 1; COMPND 2 MOLECULE: UDP-3-O-[3-HYDROXYMYRISTOYL] N-ACETYLGLUCOSAMINE COMPND 3 DEACETYLASE; COMPND 4 CHAIN: A, B; COMPND 5 SYNONYM: UDP-3-O-ACYL-GLCNAC DEACETYLASE; COMPND 6 EC: 3.5.1.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AQUIFEX AEOLICUS; SOURCE 3 ORGANISM_TAXID: 63363; SOURCE 4 STRAIN: VF5; SOURCE 5 GENE: LPXC, ENVA, AQ_1772; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS LPXC, AQUIFEX, HYDROXAMATE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR N.B.OLIVIER REVDAT 2 27-SEP-23 4OZE 1 SOURCE JRNL REMARK LINK REVDAT 1 13-AUG-14 4OZE 0 JRNL AUTH M.D.MILLER,N.GAO,P.ROSS,N.B.OLIVIER JRNL TITL MECHANISTIC INSIGHT FROM THE CRYSTAL STRUCTURE OF A.AOLICUS JRNL TITL 2 LPXC IN THE PRESENCE OF PRODUCT JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.5 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 87.76 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 92630 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 4637 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.61 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.65 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.82 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 6656 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2055 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6327 REMARK 3 BIN R VALUE (WORKING SET) : 0.2042 REMARK 3 BIN FREE R VALUE : 0.2305 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.94 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 329 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4284 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 113 REMARK 3 SOLVENT ATOMS : 598 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.31 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.85930 REMARK 3 B22 (A**2) : 2.85930 REMARK 3 B33 (A**2) : -5.71860 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.155 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.071 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.071 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.069 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.070 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 4556 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 6158 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1678 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 117 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 668 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 4556 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 3 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 557 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : 8 ; 1.000 ; HARMONIC REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 5767 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.09 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.90 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 15.64 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4OZE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-FEB-14. REMARK 100 THE DEPOSITION ID IS D_1000200325. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUL-13 REMARK 200 TEMPERATURE (KELVIN) : 140 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XSCALE REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 92692 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.610 REMARK 200 RESOLUTION RANGE LOW (A) : 87.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.40 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.61 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.30 REMARK 200 R MERGE FOR SHELL (I) : 0.73800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 0.1.29 REMARK 200 STARTING MODEL: 2GO4 REMARK 200 REMARK 200 REMARK: RICE KERNNEL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN BUFFER: 25 MM TRIS-HCL, PH REMARK 280 8.0, 0.15 M NACL, 0.1 MM ZNSO4, 5% GLYCEROL WELL SOLUTION: 15% REMARK 280 PEG 550 MME, 15% PEG 20K, 100 MM MORPHEUS BUFFER 1, 10% MORPHEUS REMARK 280 ALCHOHOLS. DROP FORMED BY 1:1 MIX, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.18433 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 82.36867 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 61.77650 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 102.96083 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 20.59217 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 LYS A 268 REMARK 465 LEU A 269 REMARK 465 THR A 270 REMARK 465 ARG A 271 REMARK 465 ASP A 272 REMARK 465 LEU A 273 REMARK 465 PRO A 274 REMARK 465 HIS A 275 REMARK 465 LEU A 276 REMARK 465 PRO A 277 REMARK 465 SER A 278 REMARK 465 VAL A 279 REMARK 465 GLN A 280 REMARK 465 ALA A 281 REMARK 465 LEU A 282 REMARK 465 MET B 1 REMARK 465 LEU B 269 REMARK 465 THR B 270 REMARK 465 ARG B 271 REMARK 465 ASP B 272 REMARK 465 LEU B 273 REMARK 465 PRO B 274 REMARK 465 HIS B 275 REMARK 465 LEU B 276 REMARK 465 PRO B 277 REMARK 465 SER B 278 REMARK 465 VAL B 279 REMARK 465 GLN B 280 REMARK 465 ALA B 281 REMARK 465 LEU B 282 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 156 CG CD CE NZ REMARK 470 GLU A 187 CG CD OE1 OE2 REMARK 470 LYS A 208 CG CD CE NZ REMARK 470 ASP A 209 CG OD1 OD2 REMARK 470 LYS B 156 CG CD CE NZ REMARK 470 LYS B 268 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 HIS A 58 7.53 86.82 REMARK 500 LEU A 99 -124.51 57.47 REMARK 500 ASN A 118 43.42 -102.23 REMARK 500 ASP A 134 116.18 -161.48 REMARK 500 GLU A 135 81.11 22.73 REMARK 500 HIS B 58 6.85 85.32 REMARK 500 LEU B 99 -125.86 57.36 REMARK 500 ASN B 118 60.83 -102.14 REMARK 500 GLU B 135 79.33 28.39 REMARK 500 ASN B 157 -163.67 -102.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 692 DISTANCE = 6.55 ANGSTROMS REMARK 525 HOH A 693 DISTANCE = 6.28 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 2 N REMARK 620 2 GLU A 120 OE1 113.0 REMARK 620 3 HIS B 29 NE2 37.6 102.5 REMARK 620 4 GLU B 90 OE1 37.4 104.5 2.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 58 NE2 REMARK 620 2 HIS A 188 NE2 112.8 REMARK 620 3 HOH A 462 O 106.3 103.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 304 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 73 OE2 REMARK 620 2 HIS A 253 NE2 99.6 REMARK 620 3 24G A 306 N11 112.4 106.0 REMARK 620 4 HOH A 713 O 107.5 134.8 96.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 74 NE2 REMARK 620 2 HIS A 226 NE2 101.7 REMARK 620 3 ASP A 230 OD1 103.2 105.3 REMARK 620 4 HOH A 713 O 103.6 125.1 114.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 58 NE2 REMARK 620 2 HIS B 188 NE2 112.4 REMARK 620 3 HOH B 461 O 107.7 106.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 73 OE2 REMARK 620 2 HIS B 253 NE2 97.9 REMARK 620 3 24G B 305 N11 112.4 107.6 REMARK 620 4 HOH B 667 O 111.9 130.7 96.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 74 NE2 REMARK 620 2 HIS B 226 NE2 102.2 REMARK 620 3 ASP B 230 OD1 102.7 106.0 REMARK 620 4 HOH B 667 O 106.4 125.0 112.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 24G A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 24G B 305 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4MDT RELATED DB: PDB REMARK 900 LPXC FROM E.COLI WITH NATIVE PRODUCT BOUND. DBREF 4OZE A 1 282 UNP O67648 LPXC_AQUAE 1 282 DBREF 4OZE B 1 282 UNP O67648 LPXC_AQUAE 1 282 SEQRES 1 A 282 MET GLY LEU GLU LYS THR VAL LYS GLU LYS LEU SER PHE SEQRES 2 A 282 GLU GLY VAL GLY ILE HIS THR GLY GLU TYR SER LYS LEU SEQRES 3 A 282 ILE ILE HIS PRO GLU LYS GLU GLY THR GLY ILE ARG PHE SEQRES 4 A 282 PHE LYS ASN GLY VAL TYR ILE PRO ALA ARG HIS GLU PHE SEQRES 5 A 282 VAL VAL HIS THR ASN HIS SER THR ASP LEU GLY PHE LYS SEQRES 6 A 282 GLY GLN ARG ILE LYS THR VAL GLU HIS ILE LEU SER VAL SEQRES 7 A 282 LEU HIS LEU LEU GLU ILE THR ASN VAL THR ILE GLU VAL SEQRES 8 A 282 ILE GLY ASN GLU ILE PRO ILE LEU ASP GLY SER GLY TRP SEQRES 9 A 282 GLU PHE TYR GLU ALA ILE ARG LYS ASN ILE LEU ASN GLN SEQRES 10 A 282 ASN ARG GLU ILE ASP TYR PHE VAL VAL GLU GLU PRO ILE SEQRES 11 A 282 ILE VAL GLU ASP GLU GLY ARG LEU ILE LYS ALA GLU PRO SEQRES 12 A 282 SER ASP THR LEU GLU VAL THR TYR GLU GLY GLU PHE LYS SEQRES 13 A 282 ASN PHE LEU GLY ARG GLN LYS PHE THR PHE VAL GLU GLY SEQRES 14 A 282 ASN GLU GLU GLU ILE VAL LEU ALA ARG THR PHE CYS PHE SEQRES 15 A 282 ASP TRP GLU ILE GLU HIS ILE LYS LYS VAL GLY LEU GLY SEQRES 16 A 282 LYS GLY GLY SER LEU LYS ASN THR LEU VAL LEU GLY LYS SEQRES 17 A 282 ASP LYS VAL TYR ASN PRO GLU GLY LEU ARG TYR GLU ASN SEQRES 18 A 282 GLU PRO VAL ARG HIS LYS VAL PHE ASP LEU ILE GLY ASP SEQRES 19 A 282 LEU TYR LEU LEU GLY SER PRO VAL LYS GLY LYS PHE TYR SEQRES 20 A 282 SER PHE ARG GLY GLY HIS SER LEU ASN VAL LYS LEU VAL SEQRES 21 A 282 LYS GLU LEU ALA LYS LYS GLN LYS LEU THR ARG ASP LEU SEQRES 22 A 282 PRO HIS LEU PRO SER VAL GLN ALA LEU SEQRES 1 B 282 MET GLY LEU GLU LYS THR VAL LYS GLU LYS LEU SER PHE SEQRES 2 B 282 GLU GLY VAL GLY ILE HIS THR GLY GLU TYR SER LYS LEU SEQRES 3 B 282 ILE ILE HIS PRO GLU LYS GLU GLY THR GLY ILE ARG PHE SEQRES 4 B 282 PHE LYS ASN GLY VAL TYR ILE PRO ALA ARG HIS GLU PHE SEQRES 5 B 282 VAL VAL HIS THR ASN HIS SER THR ASP LEU GLY PHE LYS SEQRES 6 B 282 GLY GLN ARG ILE LYS THR VAL GLU HIS ILE LEU SER VAL SEQRES 7 B 282 LEU HIS LEU LEU GLU ILE THR ASN VAL THR ILE GLU VAL SEQRES 8 B 282 ILE GLY ASN GLU ILE PRO ILE LEU ASP GLY SER GLY TRP SEQRES 9 B 282 GLU PHE TYR GLU ALA ILE ARG LYS ASN ILE LEU ASN GLN SEQRES 10 B 282 ASN ARG GLU ILE ASP TYR PHE VAL VAL GLU GLU PRO ILE SEQRES 11 B 282 ILE VAL GLU ASP GLU GLY ARG LEU ILE LYS ALA GLU PRO SEQRES 12 B 282 SER ASP THR LEU GLU VAL THR TYR GLU GLY GLU PHE LYS SEQRES 13 B 282 ASN PHE LEU GLY ARG GLN LYS PHE THR PHE VAL GLU GLY SEQRES 14 B 282 ASN GLU GLU GLU ILE VAL LEU ALA ARG THR PHE CYS PHE SEQRES 15 B 282 ASP TRP GLU ILE GLU HIS ILE LYS LYS VAL GLY LEU GLY SEQRES 16 B 282 LYS GLY GLY SER LEU LYS ASN THR LEU VAL LEU GLY LYS SEQRES 17 B 282 ASP LYS VAL TYR ASN PRO GLU GLY LEU ARG TYR GLU ASN SEQRES 18 B 282 GLU PRO VAL ARG HIS LYS VAL PHE ASP LEU ILE GLY ASP SEQRES 19 B 282 LEU TYR LEU LEU GLY SER PRO VAL LYS GLY LYS PHE TYR SEQRES 20 B 282 SER PHE ARG GLY GLY HIS SER LEU ASN VAL LYS LEU VAL SEQRES 21 B 282 LYS GLU LEU ALA LYS LYS GLN LYS LEU THR ARG ASP LEU SEQRES 22 B 282 PRO HIS LEU PRO SER VAL GLN ALA LEU HET ZN A 301 1 HET ZN A 302 1 HET ZN A 303 1 HET ZN A 304 1 HET CL A 305 1 HET 24G A 306 52 HET ZN B 301 1 HET ZN B 302 1 HET ZN B 303 1 HET CL B 304 1 HET 24G B 305 52 HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM 24G URIDINE-5'-DIPHOSPHATE-3-O-(R-3-HYDROXYMYRISTOYL)- HETNAM 2 24G GLUCOSAMINE HETSYN 24G (2R,3R,4R,5S,6R)-3-AMINO-2-{[(R)-{[(S)-{[(2R,3S,4R,5R)- HETSYN 2 24G 5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3,4- HETSYN 3 24G DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY) HETSYN 4 24G PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-5-HYDROXY-6- HETSYN 5 24G (HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-4-YL (3R)-3- HETSYN 6 24G HYDROXYTETRADECANOATE FORMUL 3 ZN 7(ZN 2+) FORMUL 7 CL 2(CL 1-) FORMUL 8 24G 2(C29 H51 N3 O18 P2) FORMUL 14 HOH *598(H2 O) HELIX 1 AA1 ARG A 49 GLU A 51 5 3 HELIX 2 AA2 VAL A 72 GLU A 83 1 12 HELIX 3 AA3 GLY A 103 LYS A 112 1 10 HELIX 4 AA4 ASN A 170 ILE A 174 5 5 HELIX 5 AA5 GLU A 185 VAL A 192 1 8 HELIX 6 AA6 ASN A 221 TYR A 236 1 16 HELIX 7 AA7 LEU A 237 GLY A 239 5 3 HELIX 8 AA8 GLY A 252 GLN A 267 1 16 HELIX 9 AA9 ARG B 49 GLU B 51 5 3 HELIX 10 AB1 VAL B 72 LEU B 82 1 11 HELIX 11 AB2 GLY B 103 LYS B 112 1 10 HELIX 12 AB3 ASN B 170 ILE B 174 5 5 HELIX 13 AB4 GLU B 185 VAL B 192 1 8 HELIX 14 AB5 ASN B 221 TYR B 236 1 16 HELIX 15 AB6 LEU B 237 GLY B 239 5 3 HELIX 16 AB7 GLY B 252 GLN B 267 1 16 SHEET 1 AA1 2 LEU A 3 VAL A 7 0 SHEET 2 AA1 2 ILE A 114 GLU A 120 -1 O ARG A 119 N GLU A 4 SHEET 1 AA2 5 LEU A 11 VAL A 16 0 SHEET 2 AA2 5 TYR A 23 PRO A 30 -1 O LEU A 26 N PHE A 13 SHEET 3 AA2 5 VAL A 87 ILE A 92 -1 O THR A 88 N HIS A 29 SHEET 4 AA2 5 ILE A 37 LYS A 41 1 N PHE A 40 O VAL A 91 SHEET 5 AA2 5 VAL A 44 PRO A 47 -1 O ILE A 46 N PHE A 39 SHEET 1 AA3 3 VAL A 53 HIS A 55 0 SHEET 2 AA3 3 ASP A 61 PHE A 64 -1 O ASP A 61 N VAL A 54 SHEET 3 AA3 3 GLN A 67 ILE A 69 -1 O ILE A 69 N LEU A 62 SHEET 1 AA4 2 PHE A 124 VAL A 125 0 SHEET 2 AA4 2 VAL A 242 LYS A 243 1 O LYS A 243 N PHE A 124 SHEET 1 AA5 5 ILE A 130 ASP A 134 0 SHEET 2 AA5 5 ARG A 137 GLU A 142 -1 O ARG A 137 N ASP A 134 SHEET 3 AA5 5 LYS A 245 PHE A 249 -1 O PHE A 249 N LEU A 138 SHEET 4 AA5 5 GLU A 148 GLU A 154 1 N GLU A 152 O SER A 248 SHEET 5 AA5 5 ARG A 161 VAL A 167 -1 O PHE A 166 N VAL A 149 SHEET 1 AA6 2 PHE A 180 PHE A 182 0 SHEET 2 AA6 2 LEU A 204 LEU A 206 1 O LEU A 206 N CYS A 181 SHEET 1 AA7 2 LEU B 3 VAL B 7 0 SHEET 2 AA7 2 ILE B 114 GLU B 120 -1 O ARG B 119 N GLU B 4 SHEET 1 AA8 5 LEU B 11 VAL B 16 0 SHEET 2 AA8 5 TYR B 23 PRO B 30 -1 O SER B 24 N GLY B 15 SHEET 3 AA8 5 VAL B 87 ILE B 92 -1 O THR B 88 N HIS B 29 SHEET 4 AA8 5 ILE B 37 LYS B 41 1 N ARG B 38 O ILE B 89 SHEET 5 AA8 5 VAL B 44 PRO B 47 -1 O ILE B 46 N PHE B 39 SHEET 1 AA9 3 VAL B 53 HIS B 55 0 SHEET 2 AA9 3 ASP B 61 PHE B 64 -1 O ASP B 61 N VAL B 54 SHEET 3 AA9 3 GLN B 67 ILE B 69 -1 O ILE B 69 N LEU B 62 SHEET 1 AB1 2 PHE B 124 VAL B 125 0 SHEET 2 AB1 2 VAL B 242 LYS B 243 1 O LYS B 243 N PHE B 124 SHEET 1 AB2 5 ILE B 130 ASP B 134 0 SHEET 2 AB2 5 ARG B 137 GLU B 142 -1 O ILE B 139 N VAL B 132 SHEET 3 AB2 5 LYS B 245 PHE B 249 -1 O PHE B 249 N LEU B 138 SHEET 4 AB2 5 GLU B 148 GLU B 154 1 N GLU B 152 O SER B 248 SHEET 5 AB2 5 ARG B 161 VAL B 167 -1 O PHE B 166 N VAL B 149 SHEET 1 AB3 2 PHE B 180 PHE B 182 0 SHEET 2 AB3 2 LEU B 204 LEU B 206 1 O LEU B 206 N CYS B 181 LINK N GLY A 2 ZN ZN A 303 1555 1555 2.12 LINK NE2 HIS A 58 ZN ZN A 302 1555 1555 2.06 LINK OE2 GLU A 73 ZN ZN A 304 1555 1555 2.04 LINK NE2 HIS A 74 ZN ZN A 301 1555 1555 2.03 LINK OE1 GLU A 120 ZN ZN A 303 1555 1555 1.93 LINK NE2 HIS A 188 ZN ZN A 302 1555 1555 2.06 LINK NE2 HIS A 226 ZN ZN A 301 1555 1555 2.01 LINK OD1 ASP A 230 ZN ZN A 301 1555 1555 2.01 LINK NE2 HIS A 253 ZN ZN A 304 1555 1555 1.95 LINK ZN ZN A 301 O HOH A 713 1555 1555 1.88 LINK ZN ZN A 302 O HOH A 462 1555 1555 2.13 LINK ZN ZN A 303 NE2 HIS B 29 2655 1555 2.04 LINK ZN ZN A 303 OE1 GLU B 90 2655 1555 1.93 LINK ZN ZN A 304 N11 24G A 306 1555 1555 2.07 LINK ZN ZN A 304 O HOH A 713 1555 1555 1.96 LINK NE2 HIS B 58 ZN ZN B 302 1555 1555 2.05 LINK OE2 GLU B 73 ZN ZN B 303 1555 1555 1.98 LINK NE2 HIS B 74 ZN ZN B 301 1555 1555 2.01 LINK NE2 HIS B 188 ZN ZN B 302 1555 1555 2.02 LINK NE2 HIS B 226 ZN ZN B 301 1555 1555 2.01 LINK OD1 ASP B 230 ZN ZN B 301 1555 1555 2.00 LINK NE2 HIS B 253 ZN ZN B 303 1555 1555 1.97 LINK ZN ZN B 301 O HOH B 667 1555 1555 1.87 LINK ZN ZN B 302 O HOH B 461 1555 1555 2.12 LINK ZN ZN B 303 N11 24G B 305 1555 1555 2.07 LINK ZN ZN B 303 O HOH B 667 1555 1555 1.93 SITE 1 AC1 5 HIS A 74 HIS A 226 ASP A 230 ZN A 304 SITE 2 AC1 5 HOH A 713 SITE 1 AC2 4 HIS A 58 HIS A 188 CL A 305 HOH A 462 SITE 1 AC3 4 GLY A 2 GLU A 120 HIS B 29 GLU B 90 SITE 1 AC4 5 GLU A 73 HIS A 253 ZN A 301 24G A 306 SITE 2 AC4 5 HOH A 713 SITE 1 AC5 5 ASN A 57 HIS A 58 PHE A 158 HIS A 188 SITE 2 AC5 5 ZN A 302 SITE 1 AC6 30 HIS A 19 ASN A 57 HIS A 58 GLU A 73 SITE 2 AC6 30 ARG A 137 TYR A 151 GLY A 153 GLU A 154 SITE 3 AC6 30 PHE A 155 THR A 179 PHE A 180 CYS A 181 SITE 4 AC6 30 GLU A 185 GLY A 195 GLY A 198 LYS A 227 SITE 5 AC6 30 ARG A 250 GLY A 251 GLY A 252 HIS A 253 SITE 6 AC6 30 ZN A 304 HOH A 713 HOH A 714 HOH A 716 SITE 7 AC6 30 HOH A 717 HOH A 718 HOH A 719 HOH A 721 SITE 8 AC6 30 HOH A 723 24G B 305 SITE 1 AC7 5 HIS B 74 HIS B 226 ASP B 230 ZN B 303 SITE 2 AC7 5 HOH B 667 SITE 1 AC8 4 HIS B 58 HIS B 188 CL B 304 HOH B 461 SITE 1 AC9 5 GLU B 73 HIS B 253 ZN B 301 24G B 305 SITE 2 AC9 5 HOH B 667 SITE 1 AD1 5 ASN B 57 HIS B 58 PHE B 158 HIS B 188 SITE 2 AD1 5 ZN B 302 SITE 1 AD2 30 24G A 306 ILE B 18 HIS B 19 ASN B 57 SITE 2 AD2 30 HIS B 58 GLU B 73 ARG B 137 TYR B 151 SITE 3 AD2 30 GLY B 153 GLU B 154 THR B 179 PHE B 180 SITE 4 AD2 30 CYS B 181 GLU B 185 ILE B 186 GLY B 198 SITE 5 AD2 30 LYS B 227 ARG B 250 GLY B 251 GLY B 252 SITE 6 AD2 30 HIS B 253 ZN B 303 HOH B 502 HOH B 664 SITE 7 AD2 30 HOH B 667 HOH B 668 HOH B 669 HOH B 670 SITE 8 AD2 30 HOH B 671 HOH B 674 CRYST1 101.332 101.332 123.553 90.00 90.00 120.00 P 61 12 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.009869 0.005698 0.000000 0.00000 SCALE2 0.000000 0.011395 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008094 0.00000